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mbase.py
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mbase.py
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"""
mbase module
This module contains the base model class from which
all of the other models inherit from.
"""
from __future__ import print_function
import abc
import sys
import os
import shutil
import threading
import warnings
import queue as Queue
from datetime import datetime
from shutil import which
from subprocess import Popen, PIPE, STDOUT
import copy
import numpy as np
from flopy import utils, discretization
from .version import __version__
from .discretization.modeltime import ModelTime
from .discretization.grid import Grid
# Global variables
iconst = 1 # Multiplier for individual array elements in integer and real arrays read by MODFLOW's U2DREL, U1DREL and U2DINT.
iprn = -1 # Printout flag. If >= 0 then array values read are printed in listing file.
class FileDataEntry(object):
def __init__(self, fname, unit, binflag=False, output=False, package=None):
self.fname = fname
self.unit = unit
self.binflag = binflag
self.output = output
self.package = package
class FileData(object):
def __init__(self):
self.file_data = []
return
def add_file(self, fname, unit, binflag=False, output=False, package=None):
ipop = []
for idx, file_data in enumerate(self.file_data):
if file_data.fname == fname or file_data.unit == unit:
ipop.append(idx)
self.file_data.append(FileDataEntry(fname, unit, binflag=binflag,
output=output, package=package))
return
class ModelInterface(object):
def __init__(self):
self._mg_resync = True
self._modelgrid = None
def update_modelgrid(self):
if self._modelgrid is not None:
self._modelgrid = Grid(proj4=self._modelgrid.proj4,
xoff=self._modelgrid.xoffset,
yoff=self._modelgrid.yoffset,
angrot=self._modelgrid.angrot)
self._mg_resync = True
@property
@abc.abstractmethod
def modelgrid(self):
raise NotImplementedError(
'must define modelgrid in child '
'class to use this base class')
@property
@abc.abstractmethod
def packagelist(self):
raise NotImplementedError(
'must define packagelist in child '
'class to use this base class')
@property
@abc.abstractmethod
def namefile(self):
raise NotImplementedError(
'must define namefile in child '
'class to use this base class')
@property
@abc.abstractmethod
def model_ws(self):
raise NotImplementedError(
'must define model_ws in child '
'class to use this base class')
@property
@abc.abstractmethod
def exename(self):
raise NotImplementedError(
'must define exename in child '
'class to use this base class')
@property
@abc.abstractmethod
def version(self):
raise NotImplementedError(
'must define version in child '
'class to use this base class')
@property
@abc.abstractmethod
def solver_tols(self):
raise NotImplementedError(
'must define version in child '
'class to use this base class')
@abc.abstractmethod
def export(self, f, **kwargs):
raise NotImplementedError(
'must define export in child '
'class to use this base class')
@property
@abc.abstractmethod
def laytyp(self):
raise NotImplementedError(
'must define laytyp in child '
'class to use this base class')
@property
@abc.abstractmethod
def hdry(self):
raise NotImplementedError(
'must define hdry in child '
'class to use this base class')
@property
@abc.abstractmethod
def hnoflo(self):
raise NotImplementedError(
'must define hnoflo in child '
'class to use this base class')
@property
@abc.abstractmethod
def laycbd(self):
raise NotImplementedError(
'must define laycbd in child '
'class to use this base class')
@property
@abc.abstractmethod
def verbose(self):
raise NotImplementedError(
'must define verbose in child '
'class to use this base class')
class BaseModel(ModelInterface):
"""
MODFLOW based models base class
Parameters
----------
modelname : string
Name of the model. Model files will be given this name. (default is
'modflowtest'
namefile_ext : string
name file extension (default is 'nam')
exe_name : string
name of the modflow executable
model_ws : string
Path to the model workspace. Model files will be created in this
directory. Default is None, in which case model_ws is assigned
to the current working directory.
"""
def __init__(self, modelname='modflowtest', namefile_ext='nam',
exe_name='mf2k.exe', model_ws=None,
structured=True, verbose=False, **kwargs):
"""
BaseModel init
"""
ModelInterface.__init__(self)
self.__name = modelname
self.namefile_ext = namefile_ext or ''
self._namefile = self.__name + '.' + self.namefile_ext
self._packagelist = []
self.heading = ''
self.exe_name = exe_name
self._verbose = verbose
self.external_path = None
self.external_extension = 'ref'
if model_ws is None: model_ws = os.getcwd()
if not os.path.exists(model_ws):
try:
os.makedirs(model_ws)
except:
print(
'\n{0:s} not valid, workspace-folder was changed to {1:s}\n'.format(
model_ws, os.getcwd()))
model_ws = os.getcwd()
self._model_ws = model_ws
self.structured = structured
self.pop_key_list = []
self.cl_params = ''
# check for reference info in kwargs
# we are just carrying these until a dis package is added
xll = kwargs.pop("xll", None)
yll = kwargs.pop("yll", None)
self._xul = kwargs.pop("xul", None)
self._yul = kwargs.pop("yul", None)
if self._xul is not None or self._yul is not None:
warnings.warn('xul/yul have been deprecated. Use xll/yll instead.',
DeprecationWarning)
self._rotation = kwargs.pop("rotation", 0.0)
self._proj4_str = kwargs.pop("proj4_str", None)
self._start_datetime = kwargs.pop("start_datetime", "1-1-1970")
# build model discretization objects
self._modelgrid = Grid(proj4=self._proj4_str, xoff=xll, yoff=yll,
angrot=self._rotation)
self._modeltime = None
# Model file information
self.__onunit__ = 10
# external option stuff
self.array_free_format = True
self.free_format_input = True
self.parameter_load = False
self.array_format = None
self.external_fnames = []
self.external_units = []
self.external_binflag = []
self.external_output = []
self.package_units = []
self._next_ext_unit = None
# output files
self.output_fnames = []
self.output_units = []
self.output_binflag = []
self.output_packages = []
return
@property
def modeltime(self):
raise NotImplementedError(
'must define modeltime in child '
'class to use this base class')
@property
def modelgrid(self):
raise NotImplementedError(
'must define modelgrid in child '
'class to use this base class')
@property
def packagelist(self):
return self._packagelist
@packagelist.setter
def packagelist(self, packagelist):
self._packagelist = packagelist
@property
def namefile(self):
return self._namefile
@namefile.setter
def namefile(self, namefile):
self._namefile = namefile
@property
def model_ws(self):
return self._model_ws
@model_ws.setter
def model_ws(self, model_ws):
self._model_ws = model_ws
@property
def exename(self):
return self._exename
@exename.setter
def exename(self, exename):
self._exename = exename
@property
def version(self):
return self._version
@version.setter
def version(self, version):
self._version = version
@property
def verbose(self):
return self._verbose
@verbose.setter
def verbose(self, verbose):
self._verbose = verbose
@property
def laytyp(self):
if self.get_package("LPF") is not None:
return self.get_package("LPF").laytyp.array
if self.get_package("BCF6") is not None:
return self.get_package("BCF6").laycon.array
if self.get_package("UPW") is not None:
return self.get_package("UPW").laytyp.array
return None
@property
def hdry(self):
if self.get_package("LPF") is not None:
return self.get_package("LPF").hdry
if self.get_package("BCF6") is not None:
return self.get_package("BCF6").hdry
if self.get_package("UPW") is not None:
return self.get_package("UPW").hdry
return None
@property
def hnoflo(self):
try:
bas6 = self.get_package("BAS6")
return bas6.hnoflo
except AttributeError:
return None
@property
def laycbd(self):
try:
dis = self.get_package("DIS")
return dis.laycbd.array
except AttributeError:
return None
# we don't need these - no need for controlled access to array_free_format
# def set_free_format(self, value=True):
# """
# Set the free format flag for the model instance
#
# Parameters
# ----------
# value : bool
# Boolean value to set free format flag for model. (default is True)
#
# Returns
# -------
#
# """
# if not isinstance(value, bool):
# print('Error: set_free_format passed value must be a boolean')
# return False
# self.array_free_format = value
#
# def get_free_format(self):
# """
# Return the free format flag for the model
#
# Returns
# -------
# out : bool
# Free format flag for the model
#
# """
# return self.array_free_format
def next_unit(self, i=None):
if i is not None:
self.__onunit__ = i - 1
else:
self.__onunit__ += 1
return self.__onunit__
def next_ext_unit(self):
"""
Function to encapsulate next_ext_unit attribute
"""
next_unit = self._next_ext_unit + 1
self._next_ext_unit += 1
return next_unit
def export(self, f, **kwargs):
"""
Method to export a model to netcdf or shapefile based on the
extension of the file name (.shp for shapefile, .nc for netcdf)
Parameters
----------
f : str
filename
kwargs : keyword arguments
modelgrid : flopy.discretization.Grid instance
user supplied modelgrid which can be used for exporting
in lieu of the modelgrid associated with the model object
Returns
-------
None or Netcdf object
"""
from .export import utils
return utils.model_export(f, self, **kwargs)
def add_package(self, p):
"""
Add a package.
Parameters
----------
p : Package object
"""
for idx, u in enumerate(p.unit_number):
if u != 0:
if u in self.package_units or u in self.external_units:
try:
pn = p.name[idx]
except:
pn = p.name
msg = "WARNING: unit {} ".format(u) + \
"of package {} already in use".format(pn)
print(msg)
self.package_units.append(u)
for i, pp in enumerate(self.packagelist):
if pp.allowDuplicates:
continue
elif isinstance(p, type(pp)):
print('****Warning -- two packages of the same type: ',
type(p), type(pp))
print('replacing existing Package...')
self.packagelist[i] = p
return
if self.verbose:
print('adding Package: ', p.name[0])
self.packagelist.append(p)
def remove_package(self, pname):
"""
Remove a package from this model
Parameters
----------
pname : string
Name of the package, such as 'RIV', 'BAS6', etc.
"""
for i, pp in enumerate(self.packagelist):
if pname.upper() in pp.name:
if self.verbose:
print('removing Package: ', pp.name)
# Remove the package object from the model's packagelist
p = self.packagelist.pop(i)
# Remove the package unit number from the list of package
# units stored with the model
for iu in p.unit_number:
if iu in self.package_units:
self.package_units.remove(iu)
return
raise StopIteration(
'Package name ' + pname + ' not found in Package list')
def __getattr__(self, item):
"""
__getattr__ - syntactic sugar
Parameters
----------
item : str
3 character package name (case insensitive) or "sr" to access
the SpatialReference instance of the ModflowDis object
Returns
-------
sr : SpatialReference instance
pp : Package object
Package object of type :class:`flopy.pakbase.Package`
Note
----
if self.dis is not None, then the spatial reference instance is updated
using self.dis.delr, self.dis.delc, and self.dis.lenuni before being
returned
"""
if item == 'output_packages' or not hasattr(self, 'output_packages'):
raise AttributeError(item)
if item == 'sr':
if self.dis is not None:
return self.dis.sr
else:
return None
if item == 'tr':
if self.dis is not None:
return self.dis.tr
else:
return None
if item == "start_datetime":
if self.dis is not None:
return self.dis.start_datetime
else:
return None
#return self.get_package(item)
# to avoid infinite recursion
if item == "_packagelist" or item == "packagelist":
raise AttributeError(item)
pckg = self.get_package(item)
if pckg is not None or item in self.mfnam_packages:
return pckg
if item == 'modelgrid':
return
raise AttributeError(item)
def get_ext_dict_attr(self, ext_unit_dict=None, unit=None, filetype=None,
pop_key=True):
iu = None
fname = None
if ext_unit_dict is not None:
for key, value in ext_unit_dict.items():
if key == unit:
iu = key
fname = os.path.basename(value.filename)
break
elif value.filetype == filetype:
iu = key
fname = os.path.basename(value.filename)
if pop_key:
self.add_pop_key_list(iu)
break
return iu, fname
def _output_msg(self, i, add=True):
if add:
txt1 = 'Adding'
txt2 = 'to'
else:
txt1 = 'Removing'
txt2 = 'from'
msg = '{} {} '.format(txt1, self.output_fnames[i]) + \
'(unit={}) '.format(self.output_units[i]) + \
'{} the output list.'.format(txt2)
print(msg)
def add_output_file(self, unit, fname=None, extension='cbc',
binflag=True, package=None):
"""
Add an ascii or binary output file file for a package
Parameters
----------
unit : int
unit number of external array
fname : str
filename of external array. (default is None)
extension : str
extension to use for the cell-by-cell file. Only used if fname
is None. (default is cbc)
binflag : bool
boolean flag indicating if the output file is a binary file.
Default is True
package : str
string that defines the package the output file is attached to.
Default is None
"""
add_cbc = False
if unit > 0:
add_cbc = True
# determine if the file is in external_units
if abs(unit) in self.external_units:
idx = self.external_units.index(abs(unit))
if fname is None:
fname = os.path.basename(self.external_fnames[idx])
binflag = self.external_binflag[idx]
self.remove_external(unit=abs(unit))
# determine if the unit exists in the output data
if abs(unit) in self.output_units:
add_cbc = False
idx = self.output_units.index(abs(unit))
# determine if binflag has changed
if binflag is not self.output_binflag[idx]:
add_cbc = True
if add_cbc:
self.remove_output(unit=abs(unit))
else:
if package is not None:
self.output_packages[idx].append(package)
if add_cbc:
if fname is None:
fname = self.name + '.' + extension
# check if this file name exists for a different unit number
if fname in self.output_fnames:
idx = self.output_fnames.index(fname)
iut = self.output_units[idx]
if iut != unit:
# include unit number in fname if package has
# not been passed
if package is None:
fname = self.name + '.{}.'.format(unit) \
+ extension
# include package name in fname
else:
fname = self.name + '.{}.'.format(package) \
+ extension
else:
fname = os.path.basename(fname)
self.add_output(fname, unit, binflag=binflag, package=package)
return
def add_output(self, fname, unit, binflag=False, package=None):
"""
Assign an external array so that it will be listed as a DATA or
DATA(BINARY) entry in the name file. This will allow an outside
file package to refer to it.
Parameters
----------
fname : str
filename of external array
unit : int
unit number of external array
binflag : boolean
binary or not. (default is False)
"""
if fname in self.output_fnames:
print("BaseModel.add_output() warning: " +
"replacing existing filename {0}".format(fname))
idx = self.output_fnames.index(fname)
if self.verbose:
self._output_msg(idx, add=False)
self.output_fnames.pop(idx)
self.output_units.pop(idx)
self.output_binflag.pop(idx)
self.output_packages.pop(idx)
self.output_fnames.append(fname)
self.output_units.append(unit)
self.output_binflag.append(binflag)
if package is not None:
self.output_packages.append([package])
else:
self.output_packages.append([])
if self.verbose:
self._output_msg(-1, add=True)
return
def remove_output(self, fname=None, unit=None):
"""
Remove an output file from the model by specifying either the
file name or the unit number.
Parameters
----------
fname : str
filename of output array
unit : int
unit number of output array
"""
if fname is not None:
for i, e in enumerate(self.output_fnames):
if fname in e:
if self.verbose:
self._output_msg(i, add=False)
self.output_fnames.pop(i)
self.output_units.pop(i)
self.output_binflag.pop(i)
self.output_packages.pop(i)
elif unit is not None:
for i, u in enumerate(self.output_units):
if u == unit:
if self.verbose:
self._output_msg(i, add=False)
self.output_fnames.pop(i)
self.output_units.pop(i)
self.output_binflag.pop(i)
self.output_packages.pop(i)
else:
raise Exception(
' either fname or unit must be passed to remove_output()')
return
def get_output(self, fname=None, unit=None):
"""
Get an output file from the model by specifying either the
file name or the unit number.
Parameters
----------
fname : str
filename of output array
unit : int
unit number of output array
"""
if fname is not None:
for i, e in enumerate(self.output_fnames):
if fname in e:
return self.output_units[i]
return None
elif unit is not None:
for i, u in enumerate(self.output_units):
if u == unit:
return self.output_fnames[i]
return None
else:
raise Exception(
' either fname or unit must be passed to get_output()')
return
def set_output_attribute(self, fname=None, unit=None, attr=None):
"""
Set a variable in an output file from the model by specifying either
the file name or the unit number and a dictionary with attributes
to change.
Parameters
----------
fname : str
filename of output array
unit : int
unit number of output array
"""
idx = None
if fname is not None:
for i, e in enumerate(self.output_fnames):
if fname in e:
idx = i
break
return None
elif unit is not None:
for i, u in enumerate(self.output_units):
if u == unit:
idx = i
break
else:
raise Exception(
' either fname or unit must be passed ' +
' to set_output_attribute()')
if attr is not None:
if idx is not None:
for key, value in attr.items:
if key == 'binflag':
self.output_binflag[idx] = value
elif key == 'fname':
self.output_fnames[idx] = value
elif key == 'unit':
self.output_units[idx] = value
return
def get_output_attribute(self, fname=None, unit=None, attr=None):
"""
Get a attribute for an output file from the model by specifying either
the file name or the unit number.
Parameters
----------
fname : str
filename of output array
unit : int
unit number of output array
"""
idx = None
if fname is not None:
for i, e in enumerate(self.output_fnames):
if fname in e:
idx = i
break
return None
elif unit is not None:
for i, u in enumerate(self.output_units):
if u == unit:
idx = i
break
else:
raise Exception(
' either fname or unit must be passed ' +
' to set_output_attribute()')
v = None
if attr is not None:
if idx is not None:
if attr == 'binflag':
v = self.output_binflag[idx]
elif attr == 'fname':
v = self.output_fnames[idx]
elif attr == 'unit':
v = self.output_units[idx]
return v
def add_external(self, fname, unit, binflag=False, output=False):
"""
Assign an external array so that it will be listed as a DATA or
DATA(BINARY) entry in the name file. This will allow an outside
file package to refer to it.
Parameters
----------
fname : str
filename of external array
unit : int
unit number of external array
binflag : boolean
binary or not. (default is False)
"""
if fname in self.external_fnames:
print("BaseModel.add_external() warning: " +
"replacing existing filename {}".format(fname))
idx = self.external_fnames.index(fname)
self.external_fnames.pop(idx)
self.external_units.pop(idx)
self.external_binflag.pop(idx)
self.external_output.pop(idx)
if unit in self.external_units:
print("BaseModel.add_external() warning: " +
"replacing existing unit {}".format(unit))
idx = self.external_units.index(unit)
self.external_fnames.pop(idx)
self.external_units.pop(idx)
self.external_binflag.pop(idx)
self.external_output.pop(idx)
self.external_fnames.append(fname)
self.external_units.append(unit)
self.external_binflag.append(binflag)
self.external_output.append(output)
return
def remove_external(self, fname=None, unit=None):
"""
Remove an external file from the model by specifying either the
file name or the unit number.
Parameters
----------
fname : str
filename of external array
unit : int
unit number of external array
"""
plist = []
if fname is not None:
for i, e in enumerate(self.external_fnames):
if fname in e:
plist.append(i)
elif unit is not None:
for i, u in enumerate(self.external_units):
if u == unit:
plist.append(i)
else:
raise Exception(
' either fname or unit must be passed to remove_external()')
# remove external file
j = 0
for i in plist:
ipos = i - j
self.external_fnames.pop(ipos)
self.external_units.pop(ipos)
self.external_binflag.pop(ipos)
self.external_output.pop(ipos)
j += 1
return
def add_existing_package(self, filename, ptype=None,
copy_to_model_ws=True):
"""
Add an existing package to a model instance.
Parameters
----------
filename : str
the name of the file to add as a package
ptype : optional
the model package type (e.g. "lpf", "wel", etc). If None,
then the file extension of the filename arg is used
copy_to_model_ws : bool
flag to copy the package file into the model_ws directory.
Returns
-------
None
"""
if ptype is None:
ptype = filename.split('.')[-1]
ptype = str(ptype).upper()
# for pak in self.packagelist:
# if ptype in pak.name:
# print("BaseModel.add_existing_package() warning: " +\
# "replacing existing package {0}".format(ptype))
class Obj(object):
pass
fake_package = Obj()
fake_package.write_file = lambda: None
fake_package.extra = ['']
fake_package.name = [ptype]
fake_package.extension = [filename.split('.')[-1]]
fake_package.unit_number = [self.next_ext_unit()]
if copy_to_model_ws:
base_filename = os.path.split(filename)[-1]
fake_package.file_name = [base_filename]
shutil.copy2(filename, os.path.join(self.model_ws, base_filename))
else:
fake_package.file_name = [filename]
fake_package.allowDuplicates = True
self.add_package(fake_package)
def get_name_file_entries(self):
"""
Get a string representation of the name file.
Parameters
----------
"""
lines = []
for p in self.packagelist:
for i in range(len(p.name)):
if p.unit_number[i] == 0:
continue
s = '{:14s} {:5d} {}'.format(
p.name[i], p.unit_number[i], p.file_name[i])
if p.extra[i]:
s += ' ' + p.extra[i]
lines.append(s)
return '\n'.join(lines) + '\n'
def has_package(self, name):
"""
Check if package name is in package list.
Parameters
----------
name : str
Name of the package, 'DIS', 'BAS6', etc. (case-insensitive).
Returns
-------
bool
True if package name exists, otherwise False if not found.
"""
if not name:
raise ValueError('invalid package name')
name = name.upper()
for p in self.packagelist:
for pn in p.name:
if pn.upper() == name:
return True
return False
def get_package(self, name):
"""
Get a package.
Parameters
----------
name : str
Name of the package, 'RIV', 'LPF', etc. (case-insensitive).
Returns
-------
pp : Package object
Package object of type :class:`flopy.pakbase.Package`
"""
if not name:
raise ValueError('invalid package name')
name = name.upper()